Torsten Seemann

`cmscan -g` is slow but will improve results due to glocal alignment and higher sensitivity

If file.fasta is a path to someone elses folder it tries to write the .fai file there and fails, when using --outseq

Metagenome mode with ALL kingdoms

3

I use your tool "Prokka" (version 1.10) with your the default rRNA predictor "Barrnap" mainly for metagenome-annotation (and am very happy with it). As my metagenomes consist of bacterial as...

Check versions of bedtools is >= 2.27

1

Needed for `-name+` option.

ENH: Add coverage to Nextclade output?

2

`Coverage` is normally defined as number of valid called bases divided by length of the virus. Does Nextclade have a column for this? The only way I can seem to...

nextclade run --output-csv is semicolon separated, not comma

9

`--output-csv` seems to be producing `;`-sep not `,`-sep The `--output-tsv` is fine. ``` % cd dattaset-dir % nextclade run --input-fasta seqiences.fasta ---dataset-dir . --output-csv out.csv % head out.csv seqName;clade;Nextclade_pango;qc.overallScore;qc.overallStatus;totalSubstitutions;totalDeletions;totalInsertions;totalFrameShifts;totalAminoacidSubstitutions;totalAminoacidDeletions;totalAmi ```

I didn't realise there was a wiki. This github README will make it much clearer where all the good information is :-) Replaces PR https://github.com/weizhongli/cdhit/pull/41

Look at Spades warning.log and do something

1

``` === Error correction and assembling warnings: * 0:00:07.339 96M / 8G WARN General (kmer_coverage_model.cpp : 367) Failed to determine erroneous kmer threshold. Threshold set to: 21 * 0:00:09.585 96M...

FLASH fails but it keeps on going: ``` [FLASH] Processed 887900 read pairs [FLASH] ERROR: Input files do not contain the same number of reads [FLASH] FLASH did not complete...

Otherwise FLASH will fail.